Security personnel confiscated the banner, and ejected four fans from the ballpark.
It did not appear that the banner was seen on television as it was unveiled inbetween the top and bottom of the fourth inning.
Sam Kennedy, the Red Sox president, made a public apology to Jones and said: "No player should have an object thrown at him on the playing field, nor be subjected to any kind of racism at Fenway Park".
Reports say there were some boos as security not only took down the sign but escorted four people from the venue.
One of the members of the group, who did not wish to be named, said they were not "not associated with any particular organization, although all of us do work as organizers in various Boston groups that combat white supremacy and racism". "Mostly groups that affiliate with racial justice causes".
One of the protesters, speaking on the condition of anonymity, said, "We see Boston continually priding itself as a kind of liberal, not racist city, and are reminded nearly constantly that it's actually an extremely segregated city".
He added that the group had been responding to the long history of white supremacy and racism across the USA that is continuing to pervade all aspects of today's American culture. And I know we have a policy that you can't affix a banner from anywhere in the ballpark.
One of those individuals spoke to The Washington Post via email, clarifying that there were actually five people involved at Fenway, with the fifth member "doing documentation across the stadium". That person reportedly "left on their own volition".
Orioles outfielder Adam Jones said he was on the receiving end of racist taunts from Red Sox fans earlier in the season. They criticised the history of the Red Sox for becoming the last team to integrate black players into the team following the end of racial segregation in Major League Baseball.